Centre for Bioinformatics, University of Oslo
The hub of bioinformatics and computational biology at the University of Oslo
Oslo, Norway
Pinned Repositories
CausalAIRR
compairr
Comparison of Adaptive Immune Receptor Repertoires
dagsim
A framework and specification language for simulating data based on graphical models
graph_peak_caller
ChIP-seq peak caller for reads mapped to a graph-based reference genome
immuneML
immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
NucBreak
Location of structural errors in a genome assembly and structural variations between a pair of genomes
NucMerge
Genome assembly quality improvement assisted by alternative assemblies and paired-end Illumina reads
numpy_alignments
Simple Python module for efficient storing and comparison of mapped reads using numpy
pyvg
Importing vg json graphs to Python data structures.
two_step_graph_mapper
Centre for Bioinformatics, University of Oslo's Repositories
uio-bmi/immuneML
immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.
uio-bmi/compairr
Comparison of Adaptive Immune Receptor Repertoires
uio-bmi/dagsim
A framework and specification language for simulating data based on graphical models
uio-bmi/graph_peak_caller
ChIP-seq peak caller for reads mapped to a graph-based reference genome
uio-bmi/CausalAIRR
uio-bmi/crypt4gh
Crypt4GH standard implementation
uio-bmi/fdr_under_dependencies
uio-bmi/kmercount
Simple kmer counter using Bloom filter and efficient hash function
uio-bmi/numpy_alignments
Simple Python module for efficient storing and comparison of mapped reads using numpy
uio-bmi/StarSignDNA
uio-bmi/immuneml_tools
Galaxy tools using the immuneML conda package.
uio-bmi/localega-broker
uio-bmi/machine_learning_in_comp_bio_exercises
These exercises are a part of the IN-BIOS5000 course at UiO, for the intro lectures on machine learning in computational biology.
uio-bmi/pharmacoepi_simulation_workshop
The material for the simulation session at the (Epi)genetics in Pharmacoepidemiology workshop
uio-bmi/statistical_genomics_exercises
uio-bmi/SynthPwr
Synthetic framework for stress testing the parameters and statistical power of epigenetic power calculators
uio-bmi/ligo
LIgO is a tool for simulation of adaptive immune receptors and repertoires.
uio-bmi/localega-tsd-proxy
uio-bmi/mq-interceptor
RabbitMQ interceptor for LocalEGA
uio-bmi/SimCal
Simulation Calibration codebase for evaluating ML pipelines between real and learned worlds
uio-bmi/tsd-file-api-client
TSD File API Client
uio-bmi/VirMake
VirMake is a Snakemake based pipeline that offers viral metagenic data analysis on paired-end data. It offers taxonomic and functional annotation, supports offline running and support for HPC cluster execution. It is made for Linux based systems and has been tested on SLURM cluster execution.
uio-bmi/cookiecutter-python-research-project
A cookiecutter for easier continous integration in a research project based on Python code
uio-bmi/IN-BIOSx000
Course material for the IN-BIOSx000 course "Sequencing technologies, data analysis, and applications" at the University of Oslo
uio-bmi/lega-uploader
LocalEGA Data Upload Tool
uio-bmi/LocalEGA-deploy-swarm-fork
Docker Swarm deployment of LocalEGA
uio-bmi/localega-proxy-webserver
uio-bmi/python-types-examples
uio-bmi/starsigndna-doc
uio-bmi/stats_for_cs
Accompanying notebooks for the new stats course for computer scientists with simulations